From 1943 to 1946, Dempster was chief physicist of the University of Chicago's Metallurgical Laboratory or "Met Lab" which integrally related to the Manhattan Project and founded to study the materials necessary for the manufacture of atomic bombs.

In 1918, Dempster developed the first modern mass spectrometer, a scientific apparatus allowing physicists to identify compounds by the mass of elements in a sample, and determine the isotopic composition of elements in a sample.[2] Dempster's mass spectrometer was over 100 times more accurate than previous versions, and established the basic theory and design of mass spectrometers that is still used to this day. Dempster's research over his career centered on the mass spectrometer and its applications, leading in 1935 to his discovery of the uranium isotope 235U.[3][4] This isotope's ability to cause a rapidly expanding fissionnuclear chain reaction allowed the development of the atom bomb and nuclear power. Dempster was also well known as an authority on positive rays.